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19,342 results for “sequence”
Measuring phylogenetic information of incomplete sequence data
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PacBio sequencing output increased through uniform and directional 5-fold concatenation
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Data from: Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence
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Strains and constructs for: A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence specific immunity against subviral parasites
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Sequence matrix and tree files for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)
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CA1 20-40 Hz oscillatory dynamics reflect trial-specific information processing supporting nonspatial sequence memory
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Sequences of the nuclear gene ADH for thirteen species of willows and two poplars: Investigating patterns of habitat specialization in fifteen co-occurring willow and poplar species.
Thirteen willow (Salix) species occur in southeastern Minnesota and often co-occur within the same wetlands. This high local diversity is challenging to explain since closely related species are often functionally similar and density-dependent interactions such as competition and susceptibility to pests and pathogens should limit their co-occurrence. However, if willow species are partitioning resources, or if they are phylogenetically structured so that closely related species rarely co-occur, then the impact of these density-dependent processes could be reduced. In this study, I examined the role of niche partitioning in maintaining local willow diversity by documenting species distributions in plots across a water availability gradient and comparing species physiology in the field and greenhouse. By taking a phylogenetic approach, I also investigated whether willow communities exhibit phylogenetic community structure and whether there is evidence for environmental filtering.
Soil Microbial Gene Sequences at the Kellogg Biological Station, Hickory Corners, MI (2004 to 2010)
Dataset Abstract Gene sequences extracted from soils. original data source http://lter.kbs.msu.edu/datasets/108
FIGURE 5 in First report of the lace bug Neoplerochila paliatseasi (Rodrigues, 1981) (Hemiptera Tingidae) infesting cultivated olive trees in South Africa, and its complete mitochondrial sequence
FIGURE 5. Usage of start codons (ATG, ATA, ATT, ATC and GTG) found in the complete complement of 13 mitochondrial protein-coding genes from 15 lace bug species belonging to the family Tingidae.
FIGURE 3 in First report of the lace bug Neoplerochila paliatseasi (Rodrigues, 1981) (Hemiptera Tingidae) infesting cultivated olive trees in South Africa, and its complete mitochondrial sequence
FIGURE 3. Percentage of maximum intragroup p-distances (K2P) in 25 species of lace bugs (Hemiptera: Tingidae). The analysis was based on a 512 bp alignment of COI barcoding sequences (n = 218).
FIGURE 2 in First report of the lace bug Neoplerochila paliatseasi (Rodrigues, 1981) (Hemiptera Tingidae) infesting cultivated olive trees in South Africa, and its complete mitochondrial sequence
FIGURE 2. Neighbor-Joining (K2P) tree of lace bugs (Hemiptera: Tingidae) based on an alignment of COI sequences (512 bp). The analysis included 218 sequences belonging to 25 species in 16 genera retrieved from BOLD, except for the newly reported Neoplerochila paliatseasi (in bold). Triangles represent collapsed groups of sequences belonging to the same species. Nodal statistical support was based on 1,000 replicates (only values> 85% are shown).
FIGURE 6 in First report of the lace bug Neoplerochila paliatseasi (Rodrigues, 1981) (Hemiptera Tingidae) infesting cultivated olive trees in South Africa, and its complete mitochondrial sequence
FIGURE 6. Predicted structure of the 22 tRNAs in the complete mitochondrial genome of Neoplerochila paliatseasi (Hemiptera: Tingidae). Inferred canonical Watson-Crick bonds are represented by lines, and non-canonical bonds (U-U, A-A, G-U, G-A, G-G, C-C, A-C, and C-U) are represented by dots.
FIGURE 7. Phylogenetic relationships among 15 in First report of the lace bug Neoplerochila paliatseasi (Rodrigues, 1981) (Hemiptera Tingidae) infesting cultivated olive trees in South Africa, and its complete mitochondrial sequence
FIGURE 7. Phylogenetic relationships among 15 lace bug species (Hemiptera: Tingidae) based on 13 mitochondrial proteincoding genes, using Bayesian inference. PCG123 was constructed using DNA sequences with partitioned codon positions. PCG12 was constructed using DNA sequences, excluding the 3rd codon position. AA was constructed using amino acid sequences. Trees were rooted by the outgroups Adelphocoris fasciaticollis and Apolygus lucorum (Miridae). Nodal statistical support is given as Bayesian posterior probability.
Autism Detection Based on Eye Movement Sequences on the Web: A Scanpath Trend Analysis Approach
<p>We propose a novel approach to detect autism based on the eye-movement paths of users on the Web. This approach based on Scanpath Trend Analysis (STA) proposed by Eraslan et al. (2016, 2017). This dataset is created to provide supplementary data for our paper entitled "Autism Detection Based on Eye Movement Sequences on the Web: A Scanpath Trend Analysis Approach" presented at <a href="http://www.w4a.info/2020/">the 17th International Web for All Conference (W4A'20)</a>. This dataset includes all the individual paths used for the evaluation of our proposed approach. The dataset also includes the Python code to re-run the evaluation.</p> <p><strong>References:</strong></p> <ul> <li>Sukru Eraslan, Yeliz Yesilada, and Simon Harper. 2016. Scanpath Trend Analysis on Web Pages: Clustering Eye Tracking Scanpaths. ACM Transactions on the Web, (SCI-E), 10, 4, Article 20.</li> <li>Sukru Eraslan, Yeliz Yesilada, and Simon Harper. 2017. Engineering web-based interactive systems: trend analysis in eye tracking scanpaths with a tolerance. In Proceedings of the ACM SIGCHI Symposium on Engineering Interactive Computing Systems (EICS '17). ACM, New York, NY, USA, 3-8.</li> </ul>
data & analysis scripts of " Behavioral effects of rhythm, carrier frequency and temporal cueing on the perception of sound sequences"
<p>Analysis scripts and data accompanying the manuscript "Behavioral effects of rhythm, carrier frequency and temporal cueing on the perception of sound sequences"</p>
Database for mi-faser: Functional sequencing read annotation for high precision microbiome analysis
<p><strong>[Database for mi-faser]</strong></p> <p><strong>mi-faser: </strong><em>microbiome - functional annotation of sequencing reads</em></p> <p>A super-fast ( < 20min/10GB of reads ) and accurate ( > 90% precision ) method for annotation of molecular functionality encoded in sequencing read data without the need for assembly or gene finding.</p> <p>Web Service: http://services.bromberglab.org/mifaser/|<br> Repository: https://bitbucket.org/bromberglab/mifaser_base/</p>
Datasets of "Whole genome sequencing of European autochthonous and commercial pig breeds provides selection signatures of adaptation of genetic resources to different breeding and production systems"
<p>Results of the F<sub>ST</sub> and H<sub>P</sub> analyses.</p>
Dataset related to article "Single-Cell Sequencing of Mouse Heart Immune Infiltrate in Pressure Overload-Driven Heart Failure Reveals Extent of Immune Activation."
<p>BACKGROUND:</p> <p>Inflammation is a key component of cardiac disease, with macrophages and T lymphocytes mediating essential roles in the progression to heart failure. Nonetheless, little insight exists on other immune subsets involved in the cardiotoxic response.</p> <p>METHODS:</p> <p>Here, we used single-cell RNA sequencing to map the cardiac immune composition in the standard murine nonischemic, pressure-overload heart failure model. By focusing our analysis on CD45<sup>+</sup> cells, we obtained a higher resolution identification of the immune cell subsets in the heart, at early and late stages of disease and in controls. We then integrated our findings using multiparameter flow cytometry, immunohistochemistry, and tissue clarification immunofluorescence in mouse and human.</p> <p>RESULTS:</p> <p>We found that most major immune cell subpopulations, including macrophages, B cells, T cells and regulatory T cells, dendritic cells, Natural Killer cells, neutrophils, and mast cells are present in both healthy and diseased hearts. Most cell subsets are found within the myocardium, whereas mast cells are found also in the epicardium. Upon induction of pressure overload, immune activation occurs across the entire range of immune cell types. Activation led to upregulation of key subset-specific molecules, such as oncostatin M in proinflammatory macrophages and PD-1 in regulatory T cells, that may help explain clinical findings such as the refractivity of patients with heart failure to anti-tumor necrosis factor therapy and cardiac toxicity during anti-PD-1 cancer immunotherapy, respectively.</p> <p>CONCLUSIONS:</p> <p>Despite the absence of infectious agents or an autoimmune trigger, induction of disease leads to immune activation that involves far more cell types than previously thought, including neutrophils, B cells, Natural Killer cells, and mast cells. This opens up the field of cardioimmunology to further investigation by using toolkits that have already been developed to study the aforementioned immune subsets. The subset-specific molecules that mediate their activation may thus become useful targets for the diagnostics or therapy of heart failure.</p> <p> </p> <p>This dataset is created in .ets form, we attach a pdf with the information about.</p>
OTUs sequences
<p>The file corresponds to sequences from 407 OTUs obtained from 16 Anopheles abdomens.</p>
NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy
<p>The data presented in "NanoGalaxy: A Galaxy tool kit with workflows for third-generation sequence analysis" to illustrate the functionality of the tools was obtained from: Wick, Ryan R., et al. "Completing bacterial genome assemblies with multiplex MinION sequencing." <em>Microbial genomics</em> 3.10 (2017).</p> <p>+</p> <p>Li, Ruichao, et al. "Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data." <em>Gigascience</em> 7.3 (2018): gix132.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.